Causal mediation analysis concerns the pathways through which a treatment affects an outcome. While most of the mediation literature focuses on settings with a single mediator, a flourishing line of research has examined settings involving multiple mediators, under which path-specific effects (PSEs) are often of interest. We consider estimation of PSEs when the treatment effect operates through K(\geq1) causally ordered, possibly multivariate mediators. In this setting, the PSEs for many causal paths are not nonparametrically identified, and we focus on a set of PSEs that are identified under Pearl's nonparametric structural equation model. These PSEs are defined as contrasts between the expectations of 2^{K+1} potential outcomes and identified via what we call the generalized mediation functional (GMF). We introduce an array of regression-imputation, weighting, and "hybrid" estimators, and, in particular, two K+2-robust and locally semiparametric efficient estimators for the GMF. The latter estimators are well suited to the use of data-adaptive methods for estimating their nuisance functions. We establish the rate conditions required of the nuisance functions for semiparametric efficiency. We also discuss how our framework applies to several estimands that may be of particular interest in empirical applications. The proposed estimators are illustrated with a simulation study and an empirical example.
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Many scientific datasets are compositional in nature. Important examples include species abundances in ecology, rock compositions in geology, topic compositions in large-scale text corpora, and sequencing count data in molecular biology. Here, we provide a causal view on compositional data in an instrumental variable setting where the composition acts as the cause. First, we crisply articulate potential pitfalls for practitioners regarding the interpretation of compositional causes from the viewpoint of interventions and warn against attributing causal meaning to common summary statistics such as diversity indices. We then advocate for and develop multivariate methods using statistical data transformations and regression techniques that take the special structure of the compositional sample space into account. In a comparative analysis on synthetic and real data we show the advantages and limitations of our proposal. We posit that our framework provides a useful starting point and guidance for valid and informative cause-effect estimation in the context of compositional data.
The key elements of seismic probabilistic risk assessment studies are the fragility curves which express the probabilities of failure of structures conditional to a seismic intensity measure. A multitude of procedures is currently available to estimate these curves. For modeling-based approaches which may involve complex and expensive numerical models, the main challenge is to optimize the calls to the numerical codes to reduce the estimation costs. Adaptive techniques can be used for this purpose, but in doing so, taking into account the uncertainties of the estimates (via confidence intervals or ellipsoids related to the size of the samples used) is an arduous task because the samples are no longer independent and possibly not identically distributed. The main contribution of this work is to deal with this question in a mathematical and rigorous way. To this end, we propose and implement an active learning methodology based on adaptive importance sampling for parametric estimations of fragility curves. We prove some theoretical properties (consistency and asymptotic normality) for the estimator of interest. Moreover, we give a convergence criterion in order to use asymptotic confidence ellipsoids. Finally, the performances of the methodology are evaluated on analytical and industrial test cases of increasing complexity.
This paper studies the classical problem of finding all $k$ nearest neighbors to points of a query set $Q$ in another reference set $R$ within any metric space. The well-known work by Beygelzimer, Kakade, and Langford in 2006 introduced cover trees and claimed to guarantee a near linear time complexity in the size $|R|$ of the reference set for $k=1$. Our previous work defined compressed cover trees and corrected the key arguments for $k\geq 1$ and previously unknown challenging data cases. In 2009 Ram, Lee, March, and Gray attempted to improve the time complexity by using pairs of cover trees on the query and reference sets. In 2015 Curtin with the above co-authors used extra parameters to finally prove a similar complexity for $k = 1$. Our work fills all previous gaps and substantially improves the neighbor search based on pairs of new compressed cover trees. The novel imbalance parameter of paired trees allowed us to prove a better time complexity for any number of neighbors $k\geq 1$.
We consider a class of statistical estimation problems in which we are given a random data matrix ${\boldsymbol X}\in {\mathbb R}^{n\times d}$ (and possibly some labels ${\boldsymbol y}\in{\mathbb R}^n$) and would like to estimate a coefficient vector ${\boldsymbol \theta}\in{\mathbb R}^d$ (or possibly a constant number of such vectors). Special cases include low-rank matrix estimation and regularized estimation in generalized linear models (e.g., sparse regression). First order methods proceed by iteratively multiplying current estimates by ${\boldsymbol X}$ or its transpose. Examples include gradient descent or its accelerated variants. Celentano, Montanari, Wu proved that for any constant number of iterations (matrix vector multiplications), the optimal first order algorithm is a specific approximate message passing algorithm (known as `Bayes AMP'). The error of this estimator can be characterized in the high-dimensional asymptotics $n,d\to\infty$, $n/d\to\delta$, and provides a lower bound to the estimation error of any first order algorithm. Here we present a simpler proof of the same result, and generalize it to broader classes of data distributions and of first order algorithms, including algorithms with non-separable nonlinearities. Most importantly, the new proof technique does not require to construct an equivalent tree-structured estimation problem, and is therefore susceptible of a broader range of applications.
DeepONets have recently been proposed as a framework for learning nonlinear operators mapping between infinite dimensional Banach spaces. We analyze DeepONets and prove estimates on the resulting approximation and generalization errors. In particular, we extend the universal approximation property of DeepONets to include measurable mappings in non-compact spaces. By a decomposition of the error into encoding, approximation and reconstruction errors, we prove both lower and upper bounds on the total error, relating it to the spectral decay properties of the covariance operators, associated with the underlying measures. We derive almost optimal error bounds with very general affine reconstructors and with random sensor locations as well as bounds on the generalization error, using covering number arguments. We illustrate our general framework with four prototypical examples of nonlinear operators, namely those arising in a nonlinear forced ODE, an elliptic PDE with variable coefficients and nonlinear parabolic and hyperbolic PDEs. While the approximation of arbitrary Lipschitz operators by DeepONets to accuracy $\epsilon$ is argued to suffer from a "curse of dimensionality" (requiring a neural networks of exponential size in $1/\epsilon$), in contrast, for all the above concrete examples of interest, we rigorously prove that DeepONets can break this curse of dimensionality (achieving accuracy $\epsilon$ with neural networks of size that can grow algebraically in $1/\epsilon$). Thus, we demonstrate the efficient approximation of a potentially large class of operators with this machine learning framework.
Moment methods are an important means of density estimation, but they are generally strongly dependent on the choice of feasible functions, which severely affects the performance. We propose a non-classical parameterization for density estimation using the sample moments, which does not require the choice of such functions. The parameterization is induced by the Kullback-Leibler distance, and the solution of it, which is proved to exist and be unique subject to simple prior that does not depend on data, can be obtained by convex optimization. Simulation results show the performance of the proposed estimator in estimating multi-modal densities which are mixtures of different types of functions.
The widespread availability of high-dimensional biological data has made the simultaneous screening of many biological characteristics a central problem in computational biology and allied sciences. While the dimensionality of such datasets continues to grow, so too does the complexity of biomarker identification from exposure patterns in health studies measuring baseline confounders; moreover, doing so while avoiding model misspecification remains an issue only partially addressed. Efficient estimators capable of incorporating flexible, data adaptive regression techniques in estimating relevant components of the data-generating distribution provide an avenue for avoiding model misspecification; however, in the context of high-dimensional problems that require the simultaneous estimation of numerous parameters, standard variance estimators have proven unstable, resulting in unreliable Type-I error control even under standard multiple testing corrections. We present a general approach for applying empirical Bayes shrinkage to variance estimators of a family of efficient, asymptotically linear estimators of population intervention causal effects. Our generalization of shrinkage-based variance estimators increases inferential stability in high-dimensional settings, facilitating the application of these estimators for deriving nonparametric variable importance measures in high-dimensional biological datasets with modest sample sizes. The result is a data adaptive approach for robustly uncovering stable causal associations in high-dimensional data in studies with limited samples. Our generalized variance estimator is evaluated against alternative variance estimators in numerical experiments. Identification of biomarkers with the proposed methodology is demonstrated in an analysis of high-dimensional DNA methylation data from an observational study on the epigenetic effects of tobacco smoking.
We consider the problem of discovering $K$ related Gaussian directed acyclic graphs (DAGs), where the involved graph structures share a consistent causal order and sparse unions of supports. Under the multi-task learning setting, we propose a $l_1/l_2$-regularized maximum likelihood estimator (MLE) for learning $K$ linear structural equation models. We theoretically show that the joint estimator, by leveraging data across related tasks, can achieve a better sample complexity for recovering the causal order (or topological order) than separate estimations. Moreover, the joint estimator is able to recover non-identifiable DAGs, by estimating them together with some identifiable DAGs. Lastly, our analysis also shows the consistency of union support recovery of the structures. To allow practical implementation, we design a continuous optimization problem whose optimizer is the same as the joint estimator and can be approximated efficiently by an iterative algorithm. We validate the theoretical analysis and the effectiveness of the joint estimator in experiments.
Discovering causal structure among a set of variables is a fundamental problem in many empirical sciences. Traditional score-based casual discovery methods rely on various local heuristics to search for a Directed Acyclic Graph (DAG) according to a predefined score function. While these methods, e.g., greedy equivalence search, may have attractive results with infinite samples and certain model assumptions, they are usually less satisfactory in practice due to finite data and possible violation of assumptions. Motivated by recent advances in neural combinatorial optimization, we propose to use Reinforcement Learning (RL) to search for the DAG with the best scoring. Our encoder-decoder model takes observable data as input and generates graph adjacency matrices that are used to compute rewards. The reward incorporates both the predefined score function and two penalty terms for enforcing acyclicity. In contrast with typical RL applications where the goal is to learn a policy, we use RL as a search strategy and our final output would be the graph, among all graphs generated during training, that achieves the best reward. We conduct experiments on both synthetic and real datasets, and show that the proposed approach not only has an improved search ability but also allows a flexible score function under the acyclicity constraint.
Discrete random structures are important tools in Bayesian nonparametrics and the resulting models have proven effective in density estimation, clustering, topic modeling and prediction, among others. In this paper, we consider nested processes and study the dependence structures they induce. Dependence ranges between homogeneity, corresponding to full exchangeability, and maximum heterogeneity, corresponding to (unconditional) independence across samples. The popular nested Dirichlet process is shown to degenerate to the fully exchangeable case when there are ties across samples at the observed or latent level. To overcome this drawback, inherent to nesting general discrete random measures, we introduce a novel class of latent nested processes. These are obtained by adding common and group-specific completely random measures and, then, normalising to yield dependent random probability measures. We provide results on the partition distributions induced by latent nested processes, and develop an Markov Chain Monte Carlo sampler for Bayesian inferences. A test for distributional homogeneity across groups is obtained as a by product. The results and their inferential implications are showcased on synthetic and real data.
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